from May to September is the rainy season in South China coast, and also the typhoon-prone season. Tropical storms and typhoons landing one after another often bring precipitation and form the heavy rain, which has a huge impact on aquaculture After rainstorm or heavy rain, the water environment of aquaculture ponds is changed greatly. Furthermore, the risk of morbidity and mortality in shrimp may be increased. The influence of severe weather on environment of shrimp pond is seldom reported.Litopenaeus vannamei culture ponds was explored from the microbiological point of view. From . The water and sediment samples were consciously collected on July 14 and 28, before and after this heavy rain. The samples were collected from semi-intensive culture ponds in which probiotics were periodically used or not. The variation of heterotrophic bacteria, in samples were investigated. Using the BIOLOG ECO microplate, the microbial community metabolic changes in water and sediment were also researched. The results showed that the number of bacteria and microbial community function had remained stable in water and sediment of the shrimp pond applied probiotics periodically before and after the heavy rainfall. in water increased, and diversity index significantly reduced in the sediment samples (<0.05) collected from the pond without applied probiotics. In additional, the carbon source utilization of microbial community in water and sediment were both changeable. Due to heavy rain, the water environment of shrimp ponds was often affected greatly. In order to cope with severe weather, the effective measures should be taken to stabilize the shrimp pond water environment and microbial ecology in both water and sediment. The probiotics, such as and so on, could be applied in the shrimp ponds periodically.